1. Understanding coexistence in high biodiversity ecosystems requires knowledge of how rare and common species share the multidimensional environmental space. Climatic and edaphic conditions can provide a plethora of habitats, supporting different compositional and structural communities where species can adapt and differentiate. 2. We used a large dataset consisting of 580 tropical tree species sampled in 163 25×25 m quadrats along an altitudinal gradient covering an area of 160 km2 of tropical rainforest in Jianfengling reserve (Hainan Island, China). For each plot the data include tree species and abundance, altitude and six soil properties from which a two dimensional environmental space was constructed. 3. With this extensive dataset we tested the hypothesis that different combination of environmental factors can generate multiple hotspots on three axes of diversity: species richness, Shannon-equivalent species richness and habitat preference, a measure of evenness in the distribution of individuals across an environmental gradient. 4. We found that humid and cool areas with more nitrogen availability were occupied by richer and more diverse communities of wide range species. Rare (in terms of number of individuals) and range restricted species instead, tended to prefer minor habitats, generally warmer with high potassium, calcium, magnesium and, in particular, phosphorous. As a result, wide and range restricted species were segregated across the environmental space. 5. Synthesis. Our findings indicate rare species tend to occur more frequently where common species are less abundant. A clear pattern of species richness and diversity was driven by a combination of several environmental factors (soil properties and climate). The complexity of the environment not only explains the different species distribution along each habitat, but also determines the relative abundance of each species in the entire community. Although some habitats have low species richness and diversity, they are highly preferred by rare species; therefore biodiversity conservation efforts should consider protecting these fragile ecosystems.